Masquerade: removing non-sample scattering from integrated reflection intensities

2012 ◽  
Vol 45 (2) ◽  
pp. 292-298 ◽  
Author(s):  
J. A. Coome ◽  
A. E. Goeta ◽  
J. A. K. Howard ◽  
M. R. Probert
Keyword(s):  
Data Collection ◽  
Diffraction Data ◽  
Low Temperatures ◽  
Test Case ◽  
X Rays ◽  
Atmospheric Conditions ◽  
X Ray Diffraction ◽  
New Approach ◽  
X Ray ◽  
Internal Agreement

X-ray diffraction experiments at very low temperatures require samples to be isolated from atmospheric conditions and held under vacuum. These conditions are usually maintainedviathe use of beryllium chambers, which also scatter X-rays, causing unwanted contamination of the sample's diffraction pattern. The removal of this contamination requires novel data-collection and processing procedures to be employed. Herein a new approach is described, which utilizes the differences in origin of scattering vectors from the sample and the beryllium to eliminate non-sample scattering. The programMasqueradehas been written to remove contaminated regions of the diffraction data from the processing programs. Coupled with experiments at different detector distances, it allows for the acquisition of decontaminated data. Studies of several single crystals have shown that this approach increases data quality, highlighted by the improvement in internal agreement factor with the test case of cytidine presented herein.

Optical and Dimensional Changes Which Accompany the Freezing and Melting of Hevea Rubber

1939 ◽  
Vol 12 (1) ◽  
pp. 18-30 ◽  
Author(s):  
W. Harold Smith ◽  
Charles Proffer Saylor
Keyword(s):  
Optical Properties ◽  
Low Temperatures ◽  
Heat Content ◽  
Uniaxial Crystal ◽  
X Rays ◽  
X Ray Diffraction ◽  
X Ray ◽  
Dimensional Changes ◽  
Ether Yield ◽  
The Individual

Abstract At suitable, low temperatures, unvulcanized rubber loses its elasticity and becomes hard and opaque. Similar changes frequently occur in baled rubber which has been tightly compressed before shipment. It is said to be frozen or “boardy.” The phenomenon has been studied by many investigators who have determined changes of volume, softening temperatures, the effects of increasing time of storage at low temperatures, the influence of pressure during freezing, and changes in heat capacity and entropy. These effects have generally been ascribed to a form of crystallization, and x-ray diffraction powder patterns indicate that crystals are present in frozen rubber. When total rubber is stretched, there are changes of volume and of heat content such as attend crystallization. With x-rays a crystal fiber pattern is obtained. It and the powder pattern obtained with frozen, compact rubber have been shown to indicate similar spacings and are assumed to be caused by the same type of crystal, the differences being ascribed to conditions of orientation. Dilute solutions of rubber hydrocarbon in ethyl ether yield small crystals of the hydrocarbon when they are subjected to temperatures between −35° and − 60° C. for several hours. The optical properties and melting points of these crystals and their x-ray diffraction patterns indicate their identity with the crystals in stretched and frozen rubber. Under the best conditions the crystals appear in spherulitic groupings, the individual needles in each spherulite having optical properties that closely approach those of a uniaxial crystal with negative elongation. The crystals of sol rubber which we obtained, melted between 9.5° and 11.0° C. Crystals of gel rubber melted between −2° and 14° C., but the melting ranges within this interval were not the same for all samples. Numerous observations have repeatedly confirmed the data. About 90 per cent of the rubber in solution may be obtained as birefringent material at −65° C. Temperatures between −40° and −50° C. have been preferred, however, because better crystals are obtained in that range.

scholarly journals HiSPoD: a program for high-speed polychromatic X-ray diffraction experiments and data analysis on polycrystalline samples

2016 ◽  
Vol 23 (4) ◽  
pp. 1046-1053 ◽  
Author(s):  
Tao Sun ◽  
Kamel Fezzaa
Keyword(s):  
Diffraction Data ◽  
High Speed ◽  
Short Pulse ◽  
Frame Rate ◽  
Short Exposure ◽  
X Rays ◽  
X Ray Diffraction ◽  
Short Exposure Time ◽  
X Ray ◽  
Structure Information

A high-speed X-ray diffraction technique was recently developed at the 32-ID-B beamline of the Advanced Photon Source for studying highly dynamic, yet non-repeatable and irreversible, materials processes. In experiments, the microstructure evolution in a single material event is probed by recording a series of diffraction patterns with extremely short exposure time and high frame rate. Owing to the limited flux in a short pulse and the polychromatic nature of the incident X-rays, analysis of the diffraction data is challenging. Here,HiSPoD, a stand-alone Matlab-based software for analyzing the polychromatic X-ray diffraction data from polycrystalline samples, is described. WithHiSPoD, researchers are able to perform diffraction peak indexing, extraction of one-dimensional intensity profiles by integrating a two-dimensional diffraction pattern, and, more importantly, quantitative numerical simulations to obtain precise sample structure information.

scholarly journals The finer things in X-ray diffraction data collection

1999 ◽  
Vol 55 (10) ◽  
pp. 1718-1725 ◽  
Author(s):  
J. W. Pflugrath
Keyword(s):  
Data Collection ◽  
Diffraction Data ◽  
Rotation Angle ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
Software Suite ◽  
X Ray ◽  
Position Sensitive ◽  
X Ray Background ◽  
Position Sensitive Detectors

X-ray diffraction images from two-dimensional position-sensitive detectors can be characterized as thick or thin, depending on whether the rotation-angle increment per image is greater than or less than the crystal mosaicity, respectively. The expectations and consequences of the processing of thick and thin images in terms of spatial overlap, saturated pixels, X-ray background andI/σ(I) are discussed. Thed*TREKsoftware suite for processing diffraction images is briefly introduced, and results fromd*TREKare compared with those from another popular package.

The structure of cubic MOF [{Ca(H2O)6}{CaGd(oxydiacetate)3}2].4H2O. A comparison between structural models obtained from Rietveld refinement of conventional and synchrotron X-ray powder diffraction data and standard refinement of single-crystal X-ray diffraction data

2012 ◽  
Vol 27 (4) ◽  
pp. 232-242 ◽  
Author(s):  
Leopoldo Suescun ◽  
Jun Wang ◽  
Ricardo Faccio ◽  
Guzmán Peinado ◽  
Julia Torres ◽  
...  
Keyword(s):  
Data Collection ◽  
Single Crystal ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Structural Models ◽  
Initial Time ◽  
High Symmetry ◽  
Powder Diffraction Data ◽  
X Ray Diffraction ◽  
X Ray

The structure of the metal–organic framework (MOF) compound [{Ca(H2O)6}{CaGd(oxydiacetate)3}2]·4H2O was determined by single-crystal X-ray diffraction and refined using conventional single-crystal X-ray diffraction data. In addition, the structure was refined using powder diffraction data collected from two sources, a conventional X-ray diffractometer in Bragg–Brentano geometry and a 12-detector high resolution synchrotron-based diffractometer in transmission geometry. Data from the latter were processed in three different ways to account for crystalline decay or radiation damage. One dataset was obtained by averaging the multiple detector patterns, another dataset was obtained by cutting the non-overlapping portions of each detector to consider only the first few minutes of data collection and a dose-corrected dataset was obtained by fitting the independent peaks in every dataset and extrapolating the intensity and peak position to the initial time of data collection or to zero-absorbed dose. The compared structural models obtained show that special processing of powder diffraction data produced a much accurate model, close to the single-crystal-based model for this particular compound with heavy atoms in high symmetry positions that do not contribute to a significant number of diffraction intensities.

A new approach to wide-angle dynamical X-ray diffraction by deformed crystals

2006 ◽  
Vol 39 (5) ◽  
pp. 652-655 ◽  
Author(s):  
S. G. Podorov ◽  
N. N. Faleev ◽  
K. M. Pavlov ◽  
D. M. Paganin ◽  
S. A. Stepanov ◽  
...  
Keyword(s):  
High Resolution ◽  
Diffraction Data ◽  
Diffraction Theory ◽  
Simple Approach ◽  
Wide Angle ◽  
X Ray Diffraction ◽  
New Approach ◽  
Dynamical Diffraction ◽  
X Ray ◽  
Distorted Waves

A new approach is proposed for X-ray dynamical diffraction theory in distorted crystals. The theory allows one to perform dynamical diffraction simulations between Bragg peaks for non-ideal crystals, using a simple approach of two distorted waves. It can be directly applied for reciprocal-space simulation. The formalism is used to analyse high-resolution X-ray diffraction data, obtained for an InSb/InGaSb/InSb/InAs superlattice grown on top of a GaSb buffer layer on a (001) GaSb substrate.

Atmospheric coherent X-ray diffraction imaging for in situ structural analysis at SPring-8 Hyogo beamline BL24XU

2018 ◽  
Vol 25 (4) ◽  
pp. 1229-1237
Author(s):  
Yuki Takayama ◽  
Yuki Takami ◽  
Keizo Fukuda ◽  
Takamasa Miyagawa ◽  
Yasushi Kagoshima
Keyword(s):  
Structural Analysis ◽  
Control Device ◽  
Photon Flux ◽  
X Rays ◽  
Atmospheric Conditions ◽  
X Ray Diffraction ◽  
Macroporous Silica ◽  
X Ray ◽  
Diffraction Imaging

Coherent X-ray diffraction imaging (CXDI) is a promising technique for non-destructive structural analysis of micrometre-sized non-crystalline samples at nanometre resolutions. This article describes an atmospheric CXDI system developed at SPring-8 Hyogo beamline BL24XU for in situ structural analysis and designed for experiments at a photon energy of 8 keV. This relatively high X-ray energy enables experiments to be conducted under ambient atmospheric conditions, which is advantageous for the visualization of samples in native states. The illumination condition with pinhole-slit optics is optimized according to wave propagation calculations based on the Fresnel–Kirchhoff diffraction formula so that the sample is irradiated by X-rays with a plane wavefront and high photon flux of ∼1 × 1010 photons/16 µmø(FWHM)/s. This work demonstrates the imaging performance of the atmospheric CXDI system by visualizing internal voids of sub-micrometre-sized colloidal gold particles at a resolution of 29.1 nm. A CXDI experiment with a single macroporous silica particle under controlled humidity was also performed by installing a home-made humidity control device in the system. The in situ observation of changes in diffraction patterns according to humidity variation and reconstruction of projected electron-density maps at 5.2% RH (relative humidity) and 82.6% RH at resolutions of 133 and 217 nm, respectively, were accomplished.

scholarly journals Use of the Bruker AXS SMART BREEZE™ System for Macromolecular X-ray Data Collection

2016 ◽  
Vol 13 (4) ◽  
Author(s):  
Christiana Standle ◽  
Blake Overson ◽  
Cody Black ◽  
Guizella Rocabado ◽  
Bruce Howard
Keyword(s):  
Data Collection ◽  
Diffraction Data ◽  
Undergraduate Research ◽  
Inorganic Compounds ◽  
Copper Anode ◽  
X Ray Diffraction ◽  
Small Unit ◽  
X Ray ◽  
Unit Cells ◽  
Protein Enzyme

The Bruker AXS SMART BREEZE™ system is a single-crystal X-ray diffractometer designed to collect data from crystals of small organic or inorganic compounds. It is typically equipped with a Molybdenum-anode sealed tube to facilitate data collection from small unit cells. We recently acquired this system, but chose to have it installed with a copper-anode sealed tube with the hope of using it to collect data from larger unit cells such as those found in crystals of proteins or other macromolecules. This is the first and only BREEZE™ system installed by Bruker AXS with a copper-anode to date. Here we show that this system is capable of efficiently collecting quality X-ray diffraction data from crystals of the enzymes lysozyme and xylanase. This capability to collect diffraction data from both macromolecular and small-molecule crystals greatly expands the scope of undergraduate research projects that can be addressed using this instrument. KEYWORDS: X-ray; Diffraction; Crystallography; Diffractometer; Protein; Enzyme; Crystal; Structure

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